Background selection in maize and humans
knitr::opts_knit$set(root.dir = '~/Documents/bgs_sims/')
knitr::opts_chunk$set(fig.width=16) Libraries and functions
library(tidyverse)
library(ggridges)
library(viridis)
library(cowplot)
orig_theme <- theme_set(theme_cowplot(font_size=20))Data preparation functions
read_sim<-function(pidata,xidata,tajdata,mu=1.66e-8,neutral=FALSE){
#read data
pi<-as.tibble(read.csv(pidata,header=T))
pi<-mutate(pi,stat=rep("pi",length(pi[,1])))
xi<-as.tibble(read.csv(xidata,header=T))
xi<-mutate(xi,stat=rep("xi",length(xi[,1])))
tajD <- as.tibble(read.csv(tajdata,header=T))
tajD<-mutate(tajD,stat=rep("tajD",length(tajD[,1])))
#munge into single tibble of means
data<-rbind(xi,pi,tajD) %>%
`colnames<-`(c("gen", 1:101, "sim", "stat")) %>%
gather(window,value,2:102) %>%
group_by(gen,stat,window) %>%
summarize(mean_val=mean(value,na.rm = T)) %>%
mutate(centimorgen=(as.numeric(window)-51)*20000*mu*100 ,mean_val=mean_val)
data=mutate(data,mean_val=if_else(centimorgen==0.00,mean_val*1.25,mean_val))
if(neutral==TRUE){
data=mutate(data,mean_val=if_else(centimorgen==0.00,mean_val/1.25,mean_val))
}
return(data)
}
#neutral=TRUE
#pidata <- "results/tennessen_neutral_pi.csv"
#xidata <- "results/tennessen_neutral_xi.csv"
#tajdata <- "results/tennessen_neutral_tajD.csv"Merge neutral and selected values
merge_sel_neutral <- function(sel_sim_data,neut_sim_data){
merged <- merge(sel_sim_data,neut_sim_data,by=c('gen','stat','window','centimorgen'))
merged <- mutate(merged,mean_val = if_else(stat=='tajD',mean_val.x-mean_val.y,mean_val.x/mean_val.y))
names(merged) <- c('gen', 'stat', 'window', 'centimorgen','bgs','neutral','mean_val')
merged
}Plot functions
Plot selection landscape
simplot<-function(somedata,mystat,label){
ggplot(filter(somedata,stat==mystat), aes(x=centimorgen, y=mean_val, group = gen,color=gen)) +
scale_color_viridis(name='Generation') +
background_grid(major = "xy", minor = "none") +
# geom_smooth(se=F) +
geom_line() +
ylab(label) + xlab("Distance (cM)") #+
# scale_x_continuous(breaks = seq(-1.5,1.5,0.5))
}
simplot_grid <- function(somedata,events,event_names,ratio=TRUE){
if (ratio == TRUE){
pi_lab <- expression(bar(pi)/bar(pi)[neut])
xi_lab <- expression(bar(xi)/bar(xi)[neut])
d_lab <- expression(bar(D)-bar(D)[neut])
}
else{
pi_lab <- expression(bar(pi))
xi_lab <- expression(bar(xi))
d_lab <- expression(bar(D))
}
legend <- get_legend(simplot(somedata,"pi",expression(bar(pi)/bar(pi)[neut]))+
theme(legend.key.height= unit(2, "cm"),
legend.title = element_text(size=16),
legend.text = element_text(size=11)) +
scale_color_viridis(name='Generation',breaks = events, labels=event_names)
)
plot_grid(
plot_grid(
simplot(somedata,"pi",pi_lab)+theme(legend.position='none'),
simplot(somedata,"xi",xi_lab)+theme(legend.position="none"),
simplot(somedata,"tajD",d_lab)+theme(legend.position="none"),
ncol = 1,
align = 'hv'),
legend, rel_widths = c(85,15))
}Function to plot ratios over time and by genetic distance
plot_ratios <- function(data,events){
comb <- data %>%
filter(window%in%c(51,51-10,51,51+10,51-20,51+20,1,101,51+5,51-5),stat%in%c('pi','xi')) %>%
mutate(centimorgen=abs(centimorgen)) %>%
group_by(centimorgen,gen,stat) %>%
summarise(mean_val=mean(mean_val))
start_val <- comb %>%
filter(gen==min(comb$gen))
ggplot(comb,aes(gen,mean_val,color=stat)) +
geom_smooth(method = 'loess',span=0.2)+
# geom_line(size=1.5) +
geom_hline(data=data.frame(yint=start_val$mean_val,centimorgen=start_val$centimorgen),aes(yintercept =yint))+
labs(x=expression(paste('Generation (x ',N[anc],')')),y=expression(x/x[neut]),color='Statistics',
caption ='Summary statistics at different distances (cM) from selected region.\nVertical lines mark demographic events. Horizontal lines denote value before demographic changes') +
# xlim(-0.1,1.25) +
facet_grid(.~centimorgen) +
geom_vline(xintercept = events, size=0.5, alpha=0.2) +
scale_color_manual(values=c("#999999", "#E69F00"),
breaks=c("pi", "xi"),
labels=c(expression(bar(pi)),expression(bar(xi)))) +
theme(strip.background = element_rect(fill=alpha('lightblue',.2)),
strip.text.y = element_text(angle = 0,hjust = 0),
plot.caption=element_text(size=12,hjust = 0)) +
scale_x_continuous(breaks=c(0,0.3,0.6,0.9,1.2))
}Function to plot absolute values over time and by genetic distance
plot_over_time <- function(data,events,stats){
comb <- data %>%
filter(window%in%c(51,51-10,51,51+10,51-20,51+20,1,101,51+5,51-5),stat==stats) %>%
mutate(centimorgen=abs(centimorgen)) %>%
group_by(centimorgen,gen,stat) %>%
summarise(neutral=mean(neutral),bgs=mean(bgs)) %>%
gather(selection,value,bgs,neutral)
start_val <- comb %>%
filter(gen==min(comb$gen))
stats_label <- c(expression(bar(stats)))
ggplot(comb,aes(gen,value,color=selection)) +
geom_line(size=1.5) +
geom_hline(data=data.frame(yint=start_val$value,centimorgen=start_val$centimorgen,sel=start_val$selection),aes(yintercept =yint,color=sel))+
labs(x=expression(paste('Generation (x ',N[anc],')')),y=stats,color='Selection')+
facet_grid(.~centimorgen) +
geom_vline(xintercept = events, size=0.5, alpha=0.2) +
scale_color_manual(values=alpha(c("#ef8a62", "#67a9cf"),.9),
breaks=c("neutral", "bgs"),
labels=c('Neutral','BGS')) +
scale_x_continuous(breaks = seq(0,2,0.5))+
theme(strip.background = element_rect(fill=alpha('lightblue',.2)),
strip.text.y = element_text(angle = 0,hjust = 0),
plot.caption=element_text(size=12,hjust = 0))
}Demographies real models
demog_torres <- read.csv('demographies/torres.csv')
demog_torres <- mutate(demog_torres,model='torres')
demog_ten <- read.csv('demographies/tennessen.csv')
demog_ten <- mutate(demog_ten,model='tennessen')
demog_maize <- read.csv('demographies/maize.csv')
demog_maize <- mutate(demog_maize,model='maize')
demog <- rbind(demog_torres,demog_ten,demog_maize)
# Torres events
anc_ext <- 0
OOA_torres <- 0.437017*2
euro_bneck_torres <- OOA_torres + 0.109481*2
torres_events <- c(anc_ext,OOA_torres,euro_bneck_torres)
torres_event_names <- c('Ancestral expansion','OoA bottleneck','Euro bottleneck')
torres_event_sizes <- c(2.10709*18449,2.10709*18449,0.322295*18449)
torres_event_end<- c(1e5,1e5,2e3)
# Tennessen events
OOA_ten <- 0.264196*2
euro_bneck_ten <-OOA_ten+ 0.0763702*2
finel_ext <-euro_bneck_ten+ 0.0502841*2
tennessen_events <- c(anc_ext,OOA_ten,euro_bneck_ten,finel_ext)
tennessen_event_sizes <- c(1.98*7310,1.98*7310,0.254609*7310,1.339863*7310)
tennessen_event_end<- c(1e5,1e5,1e5,1e3)
tennessen_event_names <- c('Ancestral expansion','OoA bottleneck','Euro bottleneck','Final growth')
# maize events
maize_events <- c(0)
maize_event_names <- c('Domestication bottleneck')Demography plot
ggplot(demog,aes(x=generation,y=N,color=model))+geom_line(size=2) +
scale_y_log10()+
scale_color_discrete(breaks=c("tennessen", "torres","maize"),labels=c('Tennessen et al.','Torres et al.','Bessinger et al.'))+
# annotate tennessen
annotate("segment", x = tennessen_events, xend = tennessen_events,
y = tennessen_event_end, yend = tennessen_event_sizes,
size=1,alpha=0.6,arrow=arrow()) +
annotate("text", x = tennessen_events, y = tennessen_event_end,
label=tennessen_event_names,
angle=c(90,90,90,0),hjust=0,vjust=c(0.5,0.5,0.5,1)) +
# annotate torres
annotate("segment", x = torres_events, xend = torres_events,
y = torres_event_end, yend = torres_event_sizes,
size=1,alpha=0.6,arrow=arrow()) +
annotate("text", x = torres_events, y = torres_event_end,
label=torres_event_names,
angle=c(90,90,0),hjust=0,vjust=c(0.5,0.5,1)) +
# annotate maize
annotate("segment", x = 0, xend = 0,
y = 12278*0.04, yend = 12278,
size=1,alpha=0.6,arrow=arrow()) +
annotate("text", x = 0, y = 12278*0.04,
label='Domestication bottleneck',
angle=0,hjust=0,vjust=1) +
labs(x=expression(paste('Generation (x ',N[anc],')')),y= "Population size",color='Demography')
ggsave('figures/annotated_demographies.pdf',width = 16)## Saving 16 x 5 in imageEuropeans
Tennessen
Neutral data
tennessen_neutral <-read_sim("results/tennessen_neutral_pi.csv",
"results/tennessen_neutral_xi.csv",
"results/tennessen_neutral_tajD.csv",
neutral=TRUE)
simplot_grid(tennessen_neutral,tennessen_events,tennessen_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
tennessen_bgs <-read_sim("results/tennessen_bgs_pi.csv",
"results/tennessen_bgs_xi.csv",
"results/tennessen_bgs_tajD.csv",
neutral=FALSE)
simplot_grid(tennessen_bgs,tennessen_events,tennessen_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
tennessen <- merge_sel_neutral(tennessen_bgs,tennessen_neutral)Plot absolute values
legend <- get_legend(plot_over_time(tennessen,tennessen_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(tennessen,tennessen_events,'pi')+theme(legend.position='none'),
plot_over_time(tennessen,tennessen_events,'xi')+theme(legend.position='none'),
plot_over_time(tennessen,tennessen_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/origVal_distance_summary_tennessen.pdf',width = 16,height = 12)Plot ratios
simplot_grid(tennessen,tennessen_events,tennessen_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/region_summary_tennessen.pdf',width = 12,heigh=9)
plot_ratios(tennessen,tennessen_events)
ggsave('figures/smooth_distance_summary_tennessen.pdf',width = 16,height = 7)Torres
Neutral data
torres_neutral <-read_sim("results/torres_neutral_pi.csv",
"results/torres_neutral_xi.csv",
"results/torres_neutral_tajD.csv",
neutral=TRUE)
simplot_grid(torres_neutral,torres_events,torres_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
torres_bgs <-read_sim("results/torres_bgs_pi.csv",
"results/torres_bgs_xi.csv",
"results/torres_bgs_tajD.csv",
neutral=FALSE)
simplot_grid(torres_bgs,torres_events,torres_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
torres <- merge_sel_neutral(torres_bgs,torres_neutral)Plot absolute values
legend <- get_legend(plot_over_time(torres,torres_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(torres,torres_events,'pi')+theme(legend.position='none'),
plot_over_time(torres,torres_events,'xi')+theme(legend.position='none'),
plot_over_time(torres,torres_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/origVal_distance_summary_torres.pdf',width = 16,height = 12)Plot ratios
simplot_grid(torres,torres_events,torres_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/region_summary_torres.pdf',width = 12,heigh=9)
plot_ratios(torres,torres_events)
ggsave('figures/smooth_distance_summary_torres.pdf',width = 16,height=7)Generic models
model1
model1_events <- c(0,0.9)
model1_event_names <- c(0,0.9)Neutral data
model1_neutral <-read_sim("results/generic/model1_neutral_pi.csv",
"results/generic/model1_neutral_xi.csv",
"results/generic/model1_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model1_neutral,model1_events,model1_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model1_bgs <-read_sim("results/generic/model1_bgs_pi.csv",
"results/generic/model1_bgs_xi.csv",
"results/generic/model1_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model1_bgs,model1_events,model1_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model1 <- merge_sel_neutral(model1_bgs,model1_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model1,model1_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model1,model1_events,'pi')+theme(legend.position='none'),
plot_over_time(model1,model1_events,'xi')+theme(legend.position='none'),
plot_over_time(model1,model1_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model1.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model1,model1_events,model1_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model1.pdf',width = 12,heigh=9)
plot_ratios(model1,model1_events)
ggsave('figures/generic_models/smooth_distance_summary_model1.pdf',width = 16,height=7)model2
model2_events <- c(0,0.5)
model2_event_names <- c('Bottleneck','Recovered')Neutral data
model2_neutral <-read_sim("results/generic/model2_neutral_pi.csv",
"results/generic/model2_neutral_xi.csv",
"results/generic/model2_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model2_neutral,model2_events,model2_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model2_bgs <-read_sim("results/generic/model2_bgs_pi.csv",
"results/generic/model2_bgs_xi.csv",
"results/generic/model2_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model2_bgs,model2_events,model2_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model2 <- merge_sel_neutral(model2_bgs,model2_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model2,model2_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model2,model2_events,'pi')+theme(legend.position='none'),
plot_over_time(model2,model2_events,'xi')+theme(legend.position='none'),
plot_over_time(model2,model2_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model2.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model2,model2_events,model2_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model2.pdf',width = 12,heigh=9)
plot_ratios(model2,model2_events)
ggsave('figures/generic_models/smooth_distance_summary_model2.pdf',width = 16,height=7)model3
model3_events <- c(0,0.6667)
model3_event_names <- c('Bottleneck','Recovered')Neutral data
model3_neutral <-read_sim("results/generic/model3_neutral_pi.csv",
"results/generic/model3_neutral_xi.csv",
"results/generic/model3_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model3_neutral,model3_events,model3_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model3_bgs <-read_sim("results/generic/model3_bgs_pi.csv",
"results/generic/model3_bgs_xi.csv",
"results/generic/model3_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model3_bgs,model3_events,model3_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model3 <- merge_sel_neutral(model3_bgs,model3_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model3,model3_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model3,model3_events,'pi')+theme(legend.position='none'),
plot_over_time(model3,model3_events,'xi')+theme(legend.position='none'),
plot_over_time(model3,model3_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model3.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model3,model3_events,model3_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model3.pdf',width = 12,heigh=9)
plot_ratios(model3,model3_events)
ggsave('figures/generic_models/smooth_distance_summary_model3.pdf',width = 16,height=7)model4
model4_events <- c(0,0.05,0.5250)
model4_event_names <- c('Bottleneck','Growth','Recovered')Neutral data
model4_neutral <-read_sim("results/generic/model4_neutral_pi.csv",
"results/generic/model4_neutral_xi.csv",
"results/generic/model4_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model4_neutral,model4_events,model4_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model4_bgs <-read_sim("results/generic/model4_bgs_pi.csv",
"results/generic/model4_bgs_xi.csv",
"results/generic/model4_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model4_bgs,model4_events,model4_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model4 <- merge_sel_neutral(model4_bgs,model4_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model4,model4_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model4,model4_events,'pi')+theme(legend.position='none'),
plot_over_time(model4,model4_events,'xi')+theme(legend.position='none'),
plot_over_time(model4,model4_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model4.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model4,model4_events,model4_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model4.pdf',width = 12,heigh=9)
plot_ratios(model4,model4_events)
ggsave('figures/generic_models/smooth_distance_summary_model4.pdf',width = 16,height=7)model5
model5_events <- c(0,0.05,0.6833)
model5_event_names <- c('Bottleneck','Growth','Recovered')Neutral data
model5_neutral <-read_sim("results/generic/model5_neutral_pi.csv",
"results/generic/model5_neutral_xi.csv",
"results/generic/model5_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model5_neutral,model5_events,model5_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model5_bgs <-read_sim("results/generic/model5_bgs_pi.csv",
"results/generic/model5_bgs_xi.csv",
"results/generic/model5_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model5_bgs,model5_events,model5_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model5 <- merge_sel_neutral(model5_bgs,model5_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model5,model5_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model5,model5_events,'pi')+theme(legend.position='none'),
plot_over_time(model5,model5_events,'xi')+theme(legend.position='none'),
plot_over_time(model5,model5_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model5.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model5,model5_events,model5_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model5.pdf',width = 12,heigh=9)
plot_ratios(model5,model5_events)## Warning: Removed 2 rows containing non-finite values (stat_smooth).
ggsave('figures/generic_models/smooth_distance_summary_model5.pdf',width = 16,height=7)## Warning: Removed 2 rows containing non-finite values (stat_smooth).model6
model6_events <- c(0.9,0.95)
model6_event_names <- c('Bottleneck','Recovered')Neutral data
model6_neutral <-read_sim("results/generic/model6_neutral_pi.csv",
"results/generic/model6_neutral_xi.csv",
"results/generic/model6_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model6_neutral,model6_events,model6_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model6_bgs <-read_sim("results/generic/model6_bgs_pi.csv",
"results/generic/model6_bgs_xi.csv",
"results/generic/model6_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model6_bgs,model6_events,model6_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model6 <- merge_sel_neutral(model6_bgs,model6_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model6,model6_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model6,model6_events,'pi')+theme(legend.position='none'),
plot_over_time(model6,model6_events,'xi')+theme(legend.position='none'),
plot_over_time(model6,model6_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model6.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model6,model6_events,model6_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model6.pdf',width = 12,heigh=9)
plot_ratios(model6,model6_events)
ggsave('figures/generic_models/smooth_distance_summary_model6.pdf',width = 16,height=7)model7
model7_events <- c(0.9,0.9667)
model7_event_names <- c('Bottleneck','Recovered')Neutral data
model7_neutral <-read_sim("results/generic/model7_neutral_pi.csv",
"results/generic/model7_neutral_xi.csv",
"results/generic/model7_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model7_neutral,model7_events,model7_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model7_bgs <-read_sim("results/generic/model7_bgs_pi.csv",
"results/generic/model7_bgs_xi.csv",
"results/generic/model7_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model7_bgs,model7_events,model7_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model7 <- merge_sel_neutral(model7_bgs,model7_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model7,model7_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model7,model7_events,'pi')+theme(legend.position='none'),
plot_over_time(model7,model7_events,'xi')+theme(legend.position='none'),
plot_over_time(model7,model7_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model7.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model7,model7_events,model7_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model7.pdf',width = 12,heigh=9)
plot_ratios(model7,model7_events)
ggsave('figures/generic_models/smooth_distance_summary_model7.pdf',width = 16,height=7)model8
model8_events <- c(0.9,0.95,0.9750)
model8_event_names <- c('Bottleneck','Growth','Recovered')Neutral data
model8_neutral <-read_sim("results/generic/model8_neutral_pi.csv",
"results/generic/model8_neutral_xi.csv",
"results/generic/model8_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model8_neutral,model8_events,model8_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model8_bgs <-read_sim("results/generic/model8_bgs_pi.csv",
"results/generic/model8_bgs_xi.csv",
"results/generic/model8_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model8_bgs,model8_events,model8_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model8 <- merge_sel_neutral(model8_bgs,model8_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model8,model8_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model8,model8_events,'pi')+theme(legend.position='none'),
plot_over_time(model8,model8_events,'xi')+theme(legend.position='none'),
plot_over_time(model8,model8_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model8.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model8,model8_events,model8_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model8.pdf',width = 12,heigh=9)
plot_ratios(model8,model8_events)
ggsave('figures/generic_models/smooth_distance_summary_model8.pdf',width = 16,height=7)model9
model9_events <- c(0.9,0.95,0.9833)
model9_event_names <- c('Bottleneck','Growth','Recovered')Neutral data
model9_neutral <-read_sim("results/generic/model9_neutral_pi.csv",
"results/generic/model9_neutral_xi.csv",
"results/generic/model9_neutral_tajD.csv",mu=1e-8,
neutral=TRUE)
simplot_grid(model9_neutral,model9_events,model9_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
BGS data
model9_bgs <-read_sim("results/generic/model9_bgs_pi.csv",
"results/generic/model9_bgs_xi.csv",
"results/generic/model9_bgs_tajD.csv",mu=1e-8,
neutral=FALSE)
simplot_grid(model9_bgs,model9_events,model9_event_names,ratio = F)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
Merge data
model9 <- merge_sel_neutral(model9_bgs,model9_neutral)Plot absolute values
legend <- get_legend(plot_over_time(model9,model9_events,'pi'))
plot_grid(ncol=2,rel_widths = c(90,10),
plot_grid(
plot_over_time(model9,model9_events,'pi')+theme(legend.position='none'),
plot_over_time(model9,model9_events,'xi')+theme(legend.position='none'),
plot_over_time(model9,model9_events,'tajD')+theme(legend.position='none'),
nrow = 3,align = 'hv',axis = 'lb'),
legend)
ggsave('figures/generic_models/origVal_distance_summary_model9.pdf',width = 16,height = 12)Plot ratios
simplot_grid(model9,model9_events,model9_event_names,ratio = T)## Scale for 'colour' is already present. Adding another scale for
## 'colour', which will replace the existing scale.
ggsave('figures/generic_models/region_summary_model9.pdf',width = 12,heigh=9)
plot_ratios(model9,model9_events)## Warning: Removed 1 rows containing non-finite values (stat_smooth).
ggsave('figures/generic_models/smooth_distance_summary_model9.pdf',width = 16,height=7)## Warning: Removed 1 rows containing non-finite values (stat_smooth).